This 1994-era engine was pulled from my boat and is in my shop. As an exercise, I am taking it apart and trying to figure out what is wrong. I have no experience with diesel engines but have time, space and the manual.

The symptoms when the engine was pulled are:
1) engine ran roughly with unburned fuel in the exhaust and much smoke.
2) I determined one cylinder was not firing using the decompression levers.
3) If I switched injectors on the non-working cylinder with another injector from a working cylinder, the original non-working cylinder continued not working and the other cylinder worked as before. Thus the injectors seem fine.

My first thought was maybe a problem with the valves associated with the rocker-arm assembly. Once I got the valve cover off, I manually spun the crankshaft and observed the valve movements. Everything looked identical on all three cylinders. No obvious problem here.

Next, I proceeded to removed the engine head. I have attached two pictures - one shows the bottom of the head and the other shows the pistons. The "bad" cylinder is marked in the photos.

My observations:
- both parts are covered in black carbon soot. Is this normal or a sign of the age of the engine.
- the "bad" piston has slightly different wear marks on the top from the other two but I don't know what this means.
- all three pistons move as expected when I rotate the crankshaft. However, the piston in the "bad" cylinder might not lift as high as the other two. The other two pistons essentially are flat with the top of the engine surface at their maximum height. The suspect piston might be a 1/16th or so below this height. However, any difference is not obvious to my eye.

Otherwise - all looks OK.

Does anyone have any advice what to look for next? I thought I would probably have located the problem by now...

It may look like there is a rust stain on the bad cylinder gasket surface? It could have bent a rod. It takes very little loss of comrpression to make a diesel not fire and 1/16" is a lot. A little water in there could do that.

Take a 1/3 cup of oil and pour it into the bad cylinder and go away for 4-6 hours. after 6 hours (or overnight) is the oil level down lots or drained out. A tight piston will hardly leak a drop of oil. Broken rings will cause the oil to fall over a few hours.

If so you have a broken ring or rings. The 1993-1994 yanmar gm series had a bad batch of pistons which tend to break a ring land or two which causes the rings to break also. Look for scuffing at the sides of the bad cylinder.

There appears to be an imprint of a valve head on the top of the "not firing" piston and there are some markings on/around the "not firing" valve and head. I would focus my attention on this valve - spring ok etc.

First, well done for the diagnostics you have performed so far. Much better than many I have seen.

Well looking at this I am surprised it ran at all. Particularly the middle pot which appears to have a gasket burn through on the head face next to the precombustion chamber.

Anyway, assuming that pot was still firing I'd say the brown marks next to the intake valve on the non firing chamber is a clue that the valve may no longer be sealing properly. Bent or burned. But I would also suggest carefully feeling the bores of each of the piston sleeves to see if there is a marked difference in their condition, such as scoring or glazing on the pot that is not firing.

Finally, is it certain that the engine was down to two pots ALL of the time or just at low revs, as if it was the latter this would certainly indicate a loss of compression on that third piston (consistent with both valve seat problems and worn/damaged rings).

Keep us posted, love to hear how it turns out.

P.S. I am sure you are aware of this but be careful turning things over with all that loose crud around, still quite easy to do more damage if a flake of rusted gasket drops down between the piston and sleeve. I have forced myself to clean everything very carefully BEFORE I start playing these days.

Forgot to mention that you can and should check the valve sealing by pouring some diesel into the intake and exhaust ports (the valve stem side) and see if it leaks through into the combustion chamber. Generally speaking, a drip is not acceptable, but a moistening of the junction between valve head and valve seat is.

If the piston is not coming to the top of the cylinder most likely water has entered the cylinder and bent the rod and rusted or bent the valve you MUST find the cause,in the photo it looks like there may have been a leak between the water jacket and cylinder(upper right )look very closely at the gasket, head and block after cleaning
In the photo of the block I can not tell if that is an imprint of the valve or reflection?
If it is an imprint you need to find the cause of valve hitting the piston!!!!!!

The head shows similar carbon buildup for all cylinders, indicating they were all firing at least reasonably well (assuming this symptom has been evident for quite a while). So I would also be asking if the problem was only at idle, which would indicate low compression as the probable cause.

As already noted, the first photograph looks like the piston has an impression from valve strike .... similar size and position. As suggested above I would use fluids to test for leaks at the rings and valve seals before stripping down.

For the 1/16th inch lower piston height, have you measured this? It's easy with a straight edge and feeler gauges. If it really is 1/16th inch, that is a lot and suggests either an incorrect part fitted or something bent inside.

You might take the cylinder head, pistons, rods and rockers to a machine shop that specializes in cylinder head refurbishing. They can bench test, diagnose and repair as needed. I would replace any suspect parts at that time and re-install, should fix the problem. Good luck!

You should have checked compression first before shooting yourself in the foot with destructive disassembling. If torque of that cylinder’s injector line adapter at injector pump is at an incorrect torque engine will perform as you describe. This individual cylinder's fuel flow can only be adjusted with pump on a test stand or when it is operating under cruise power loads.

This injector pump has three separate pump pistons inside one for each cylinder. Sometimes when bleeding air from engine injector line at pump adapter can be loosened, If this is done without using two wrenches to prevent adapter from changing its torque fuel pressure to that cylinder will change.

While cylinder head is removed it is a good time to flood valve cavities with gasoline to test for valve leakage.

I applaud you for attempting to learn about diesel engines and your engine in particular. I suggest you find someone who knows diesel engines and get some coaching and guidance. But by all means, if you continue to disassemble your engine, mark where all of your piston rods, main bearing caps, ect. face and go. These things are machined in a particular way and need reassembled in the right place and direction. Good luck !